Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with build-in screening functionality for DelHV69/70- and N501Y variants such as B.1.1.7

Nörz, Dominik; Grunwald, Moritz; Olearo, Flaminia; Fischer, Nicole; Aepfelbacher, Martin; Pfefferle, Susanne; Lütgehetmann, Marc

doi:10.1101/2021.02.12.21251614

Cited by 3 publications

(3 citation statements)

References 11 publications

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“…Furthermore, the SARS-CoV-2 variant of concern (VOC) B.1.1.7 was detected [16], and it was confirmed that other family members also tested positive for B.1.1.7.…”

Section: Case-reportmentioning

confidence: 77%

Fatal outcome of SARS-CoV-2 infection (B1.1.7) in a 4-year-old child

et al. 2021

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This case report highlights details of a case of critical acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) with B1.1.7 variant in a 4-year-old girl who died due to pneumonia and pulmonary hemorrhage. The girl was referred to our University ECMO Center from another University hospital for veno-arterial extracorporeal membrane oxygenation (VA-ECMO). In the clinical course, superinfection with Pseudomonas aeruginosa was detected. Virological evidence of herpes simplex sepsis was also obtained in blood samples on her day of death. Transcription polymerase chain reaction (PCR) confirmed SARS-CoV-2 infection in lung tissue. Postmortem computed tomography showed pulmonary hemorrhage with inhomogeneous density values in both lungs. Lung tissue showed no ventilated areas. Autopsy revealed a massively congested lung with evidence of acute respiratory distress syndrome (ARDS) and pneumonia with multiple abscesses. Histopathology showed a mixture of diffuse alveolar injury with hyaline membranes, massive hemorrhage, and bronchopneumonia with multiple granulocytic abscesses. Cardiac examination revealed pericarditis. Suspicion of myocarditis or myocardial infarction could not be confirmed microscopically. To our knowledge, this is the first autopsy-based case report of the death of a previously healthy child due to the new variant B 1.1.7 in Germany.

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“…Furthermore, the SARS-CoV-2 variant of concern (VOC) B.1.1.7 was detected [16], and it was confirmed that other family members also tested positive for B.1.1.7.…”

Section: Case-reportmentioning

confidence: 77%

Fatal outcome of SARS-CoV-2 infection (B1.1.7) in a 4-year-old child

et al. 2021

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“…Several groups have described publicly available RT-qPCR protocols for detection of lineage B.1.1.7 that can be divided into SNP genotyping assays using either SYBR- [41] or probe-based [42] melting curve analyses, multiplexed probe-based RT-qPCR [43][44][45][46], and a combination of target drop-out tests [47]. While these open source RT-qPCR protocols offer cost-effective, rapid strategies to directly detect multiple SARS-CoV-2 variants, some are limited by only assessing a small number of mutations that preclude identification of specific variants and most have yet to be tested in real world surveillance scenarios.…”

Section: Republicmentioning

confidence: 99%

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Kovacova

Boršová

Paul

et al. 2021

Preprint

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The recent emergence of a novel variant of SARS-CoV-2 called lineage B.1.1.7 has sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating worldwide efforts to detect and track the variant. Current approaches to detect the B.1.1.7 variant include sequencing and molecular tests that contain a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack a robust genomic surveillance program and the failed target assays detect multiple unrelated variants that contain similar mutations as B.1.1.7, there is an urgent need to develop molecular tests that can accurately and rapidly identify the B.1.1.7 variant. We have developed a room temperature-stable, multiplexed RT-qPCR test that readily differentiates the B.1.1.7 variant from the most common SARS-CoV-2 variants. The test consists of two assays that target either the common SARS-CoV-2 spike gene or the two deletions in the spike gene (ΔH69/ΔV70 and ΔY144) that are present in the B.1.1.7 variant. Moreover, a simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the ΔH69/ΔV70 deletion. Each assay is multiplexed with a human RNase P internal control to assess RNA extraction and assay performance. This test can easily be implemented in diagnostic labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.

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“…Nasopharyngeal swabs withdrawal and analysis for SARS-CoV-2 RNA were performed as recently described [20]. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) for N501Y and del HV69/70 as described elsewhere in a combination with commercially available assays screening for E484K and P681H (TIB Molbiol, Berlin, Germany) as recommended by the manufacturer was additionally done to screen for the VOC-202012/01 lineage [21].…”

Section: Rt-pcr For Sars-cov-2mentioning

confidence: 99%

Dying of VOC-202012/01 — multimodal investigations in a death case of the SARS-CoV-2 variant

et al. 2021

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The current pandemic with Severe acute respiratory syndrome-coronavirus-2 has been taking on new dynamics since the emergence of new variants last fall, some of them spreading more rapidly. Many countries currently find themselves in a race to ramp up vaccination strategies that have been initiated and a possible third wave of the pandemic from new variants, such as the Variant of Concern-202012/01 from the B.1.1.7 lineage. Until today, many investigations in death cases of Coronavirus-disease-19 have been conducted, revealing pulmonary damage to be the predominant feature of the disease. Thereby, different degrees of macroscopic and microscopic lung damage have been reported, most of them resembling an Acute Respiratory Distress Syndrome. Far more, systemic complications of the disease such as pulmonary embolisms have been described. However, neither morphologic nor virologic findings of patients dying of the new variants have yet been reported. Here, we report on a comprehensive analysis of radiologic, morphologic, and virologic findings in a fatal case of this variant.

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Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with build-in screening functionality for DelHV69/70- and N501Y variants such as B.1.1.7

Cited by 3 publications

References 11 publications

Fatal outcome of SARS-CoV-2 infection (B1.1.7) in a 4-year-old child

Fatal outcome of SARS-CoV-2 infection (B1.1.7) in a 4-year-old child

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Dying of VOC-202012/01 — multimodal investigations in a death case of the SARS-CoV-2 variant

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